Christoph Gohlke

Not sure this is helpful: the file `gray.movie.u2.tif` contains more than 2^16 IFDs. Such files are not uncommon in bio-imaging. Some libraries (e.g. libtiff) can not access all IFDs because...

FWIW, the excessive peak memory usage during encoding can be reproduced using libjxl 0.6.1 via the Python [imagecodecs](https://pypi.org/project/imagecodecs/) package. Decoding to uint8 buffer looks reasonable: ```Python import psutil from imagecodecs...

The crash is in `tetgenmesh::orient3dfast` when indexing `pd[0]`, which is not valid. The `tetgenmesh::incrementaldelaunay` passes `permutarray[i]` with `i=3` to `tetgenmesh::orient3dfast`, but `permutarray` is only allocated for 3 points. ``` _tetgen.cp36-win_amd64.pyd!tetgenmesh::orient3dfast(double...

``` -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= bcolz version: 1.1.3.dev11 NumPy version: 1.13.3 Blosc version: 1.11.2 ($Date:: 2017-01-27 #$) Blosc compressors: ['blosclz', 'lz4', 'lz4hc', 'snappy', 'zlib', 'zstd'] Numexpr version: 2.6.4 Dask version: 0.16.0 Python version:...

> Could you please try to add the fix in commit e39dcc1 and see if that fixes the issue? Thanks in advance. That fixes the segfaults. Thank you.

Well, this is Cygwin, which should behave like Linux. It seems that `HAVE_ISNAN` is defined even though the Cygwin headers don't have a `isnan` function. Probably better to install the...

FWIW, `006388_0.tif` is not really a WSI, more a regular TIFF: no pyramid levels, wrong resolution metadata, small tiles, ZIP compression, horizontal predictor.

Here's the relevant section from the [TIFF Technical Note #2](https://gitlab.com/libtiff/libtiff/-/blob/master/doc/specification/technote2.rst#L238-274): What data is being compressed? ------------------------------ In lossy JPEG compression, it is customary to convert color source data to YCbCr...

```Python In [4]: da.from_zarr(t.series[0].levels[0].aszarr()) ValueError: not enough values to unpack (expected 2, got 1) ``` To access the first level of the first multi-resolution series as zarr array, not group,...

SCN containing Z-stacks are not supported yet by tifffile. Can you please provide a sample file?